The former Burnley stopper joined Villa over the summer, and was called up to the England squad alongside Tyrone Mings for the second time this season last week.
However, the England national team have since confirmed that he won't be linking up with the squad for their upcoming Euro 2020 qualifiers against the Czech Republic and Bulgaria.
Sheffield United goalkeeper Dean Henderson has replaced Heaton for the Three Lions.
There is no word on the severity of the injury sustained by the 33-year-old, although England confirmed that it was picked up by the goalkeeper during Villa's 5-1 win at Norwich on Saturday. Heaton played the full 90 minutes.
Villa's next fixture is up against Brighton on October 19, should Heaton miss that encounter, Jed Steer would step in having featured in each of Villa's Carabao Cup wins so far this campaign.